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Detailed information for vg0415909654:

Variant ID: vg0415909654 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 15909654
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGCCGTGCCTCTTCTTAGATGGTGTCATCCTCATAGGCTGCCATCGCCGCCATGACCATGGTGATCAAGGAGGTTATCTCTTTCTTCGCACCTGCCTCT[G/A]
CTGCCCTCATCCGAGTCGTCAGCCTCGTTGCCACTTTTGTCCTCGTTCTATTCCTTCAGCGATAGTGGGCCCTCGTTGGAGTCCTTTGATAGGACCTGTT

Reverse complement sequence

AACAGGTCCTATCAAAGGACTCCAACGAGGGCCCACTATCGCTGAAGGAATAGAACGAGGACAAAAGTGGCAACGAGGCTGACGACTCGGATGAGGGCAG[C/T]
AGAGGCAGGTGCGAAGAAAGAGATAACCTCCTTGATCACCATGGTCATGGCGGCGATGGCAGCCTATGAGGATGACACCATCTAAGAAGAGGCACGGCTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.30% 6.10% 1.67% 0.00% NA
All Indica  2759 98.70% 0.40% 0.94% 0.00% NA
All Japonica  1512 79.00% 17.70% 3.31% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.10% 0.00% 2.86% 0.00% NA
Indica II  465 97.60% 1.90% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.30% 0.89% 0.00% NA
Temperate Japonica  767 63.40% 32.30% 4.30% 0.00% NA
Tropical Japonica  504 98.40% 0.60% 0.99% 0.00% NA
Japonica Intermediate  241 88.40% 6.60% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 3.33% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0415909654 G -> A LOC_Os04g26890.1 downstream_gene_variant ; 4230.0bp to feature; MODIFIER silent_mutation Average:64.553; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0415909654 G -> A LOC_Os04g26890-LOC_Os04g26910 intergenic_region ; MODIFIER silent_mutation Average:64.553; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0415909654 NA 1.39E-07 mr1229 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 5.89E-07 mr1880 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 7.75E-07 mr1045_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 3.68E-07 mr1229_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 6.32E-06 mr1555_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 1.23E-06 mr1596_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 8.90E-09 mr1748_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 2.84E-06 mr1748_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 6.22E-07 mr1763_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0415909654 NA 8.30E-06 mr1865_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251